Exact rotamer optimization for protein design

Computational methods play a central role in the rational design of novel proteins. The present work describes a new hybrid exact rotamer optimization (HERO) method that builds on previous dead-end elimination algorithms to yield dramatic performance enhancements. Measured on experimentally validated physical models, these improvements make it possible to perform previously intractable designs of entire protein core, surface, or boundary regions. Computational demonstrations include a full core design of the variable domains of the light and heavy chains of catalytic antibody 48G7 FAB with 74 residues and 10(128) conformations, a full core/boundary design of the beta1 domain of protein G with 25 residues and 10(53) conformations, and a full surface design of the beta1 domain of protein G with 27 residues and 10(60) conformations. In addition, a full sequence design of the beta1 domain of protein G is used to demonstrate the strong dependence of algorithm performance on the exact form of the potential function and the fidelity of the rotamer library. These results emphasize that search algorithm performance for protein design can only be meaningfully evaluated on physical models that have been subjected to experimental scrutiny. The new algorithm greatly facilitates ongoing efforts to engineer increasingly complex protein features.     

The identification of nitrated polycyclic aromatic hydrocarbons in diesel particulate extracts and their potential formation as artifacts during particulate collection

Summary The highly complex matrix of diesel particulate extracts was analyzed for nitrated polycyclic aromatic hydrocarbons (nitro-PAH) using fused-silica capillary-column gas chromatography along with a thermionic nitrogen-phosphorus detector (TID) and high-performance liquid chromatography followed by on-line catalytic reduction of the nitro-PAH to amino-PAH and subsequent fluorescence detection. Positive isomer identification and quantitation of nitro-PAH are from retention times of authentic standards and their mass spectra. The ease of nitro-PAH formation by nitration of PAH raises the question regarding the origin of these species, whether they are produced as “native” products during the engine combustion process and/or in the exhaust, or instead, formed as the result of chemical conversion to produce artifacts during the sampling procedure. This problem is assessed examing 1-nitropyrene-concentration in particulates of three light-duty diesel engines for different sampling times. 1-Nitropyrene concentrations show only a moderate increase with sampling time under average sampling conditions. Presented at the 15th International Symposium on Chromatography, Nürnberg, October 1984     

Application of HPLC to measure vanadium in environmental,biological and clinical matrices

Vanadate and vanadium compounds exist in many environmental, biological and clinical matrices, and despite the need only limited progress has been made on the analysis of vanadium compounds. The vanadium coordination chemistry of different oxidation states is known, and the result of the characterization and speciation analysis depends on the subsequent chemistry and the methods of analysis. Many studies have used a range of methods for the characterization and determination of metal ions in a variety of materials. One successful technique is high performance liquid chromatography (HPLC) that has been used mainly for measuring total vanadium level and metal speciation. Some cases have been reported where complexes of different oxidation states of vanadium have been separated by HPLC. Specifically reversed phase (RP) HPLC has frequently been used for the measurement of vanadium. Other HPLC methods such as normal phase, anion-exchange, cation-exchange, size exclusion and other RP-HPLC modes such as, ion-pair and micellar have been used to separate selected vanadium compounds. We will present a review that summarizes and critically analyzes the reported methods for analysis of vanadium salts and vanadium compounds in different sample matrices. We will compare various HPLC methods and modes including sample preparation, chelating reagents, mobile phase and detection methods. The comparison will allow us to identify the best analytical HPLC method and mode for measuring vanadium levels and what information such methods provide with regard to speciation and quantitation of the vanadium compounds.     

Cooling of Al-Cu-Fe-Cr-Ni high entropy alloy with different size

Cooling rate is critical in synthesizing nanoparticles (NPs), which determines the microstructure and the corresponding mechanical, thermal and electrical properties. This research, as the most initiative one, studies microstructure formation of three different sized high entropy alloy (HEA) NPs under three different cooling rates, employing molecular dynamics (MD). Through analysis of potential energy, “common neighbor analysis”, radial distribution function, and also the mean square displacement, it is found that phase transition temperature is independent of HEA NP size, and as cooling rate decrease, more amorphous atoms transform to fcc and hcp orders, which can alternate the mechanical and thermodynamic properties of the final structure. The Cr atoms are found to aggregate into one cluster inside the NP and also try to migrate to the surface of the HEA NP, due to the large diffusivity. This research provides new insights in the size dependency of the nanoparticles, which may motivate more applications in which the strong size dependency is not desirable.     

Ultrasonic assisted synthesis of nanocrystalline cellulose as support and reducing agent for Ag nanoparticles: green synthesis and novel effective nanocatalyst for degradation of organic dyes

In this study, nanocrystalline cellulose (NCC) prepared from microcrystalline cellulose using high‐intensity ultrasonication as mechanical method without any chemical treatment. The obtained NCC with around 30–50 nm diameters, utilized as support, reducing and stabilizing agent for in‐situ green and eco‐friendly synthesis of silver nanoparticles (Ag NPs). The catalytic activity of composite was examined for degradation of environmental pollutants. The structure of as‐synthesized composite (Ag@NCC) was characterized by ultraviolet–visible spectroscopy (UV–vis), field emission scanning electron microscopy (FE‐SEM); Transmission electron microscopy (TEM); Energy dispersive spectroscopy (EDS), Fourier transform infrared spectroscopy (FT‐IR), X‐ray diffraction (XRD) and thermogravimetric analysis (TGA). The results of the catalytic reaction experiments showed that spherically shaped silver nanoparticles of around 20 nm distributed on the surface of nanocellulose demonstrated high catalytic efficiency towards the removal of methyl orange (MO) and 4‐nitrophenol (4‐NP).     

Enantioresolution of 2-methoxy-2-(1-naphtyl)propionic acid using diastereomeric salt formation with chiral phenylethylamine

An enantioresolution of 2-methoxy-2-(1-naphtyl)propionic acid (MαNP acid) using the diastereomeric salt with chiral (R)-phenylethylamine was achieved to give enantiopure (R)-MαNP acid in 29% yield with >99% ee based on rac-MαNP acid. X-ray crystallographic analysis of diastereomeric salt revealed that (R)-MαNP acid was tightly arranged by four independent hydrogen bonds and one CH–π interaction with (R)-phenylethylamine.     

用HIFN 5NP4GS3网络处理器设计8Gbit/s线速路由器

介绍了使用5NP4GS3网络处理器设计的准交换结构8Gb／8线速路由器。HIFN公司的5NP4G3是OC-48级别网络处理器中综合性能最佳的一个芯片产品,准交换结构设计充分挖掘了这颗处理器能力,使设计具有很高的性价比。文章给出了路由器各个部分的设计,经过实际测试,证明了系统设计的正确性和可靠性。     

Mutual solubilities of hydrocarbons and water with the CPA EoS

The knowledge of hydrocarbon/water phase equilibria is important in the design and operation of equipment for petroleum transport and refining and petrochemical plants. The presence of water in a hydrocarbon mixture can affect the product quality and damage the operation equipment due to corrosion and formation of gas hydrates. Tracing the concentration of hydrocarbons in aqueous media is also important for technical purposes like preventing oil spills and for ecological concerns such as predicting the fate of these organic pollutants in the environment.     

基于网络处理器IXP2400的组播包高速转发技术

传统的IP报文的组播技术,由于在处理过程中需要把整个报文的内容报文复制多份,因此处理器需要对缓存报文的外部存储空间进行多次I/O操作,这严重制约了当前处理器,特别是网络处理器的高速报文处理能力,转发效率不高.为此,提出了一种新的技术--"零拷贝"转发技术.该技术只修改报文头,报文体不复制,减少了大量的I/O操作,提高了转发效率.     

The K-SAT Problem in a Simple Limit

In this work we compute the thermodynamic properties of the 3-satisfiability problem in the infinite connectivity limit. In this limit the computation can be strongly simplified and the thermodynamic properties can be obtained with a high accuracy. We find evidence for a continuous replica symmetry breaking in the region of high number of clauses, >_c.